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- PDB-3gqg: Crystal structure at acidic pH of the ferric form of the Root eff... -

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Basic information

Entry
Database: PDB / ID: 3gqg
TitleCrystal structure at acidic pH of the ferric form of the Root effect hemoglobin from Trematomus bernacchii.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / pentacoordinate high-spin Fe(III) form / antacrtic fish hemoglobin / Acetylation / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / oxygen carrier activity / hydrogen peroxide catabolic process / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / oxygen carrier activity / hydrogen peroxide catabolic process / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsVergara, A. / Franzese, M. / Merlino, A. / Bonomi, G. / Mazzarella, L.
CitationJournal: Biophys.J. / Year: 2009
Title: Correlation between hemichrome stability and the root effect in tetrameric hemoglobins.
Authors: Vergara, A. / Franzese, M. / Merlino, A. / Bonomi, G. / Verde, C. / Giordano, D. / di Prisco, G. / Lee, H.C. / Peisach, J. / Mazzarella, L.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1398
Polymers63,6734
Non-polymers2,4664
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-105 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.720, 94.780, 61.720
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211
Detailstetramer

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Components

#1: Protein Hemoglobin subunit alpha / Hemoglobin alpha chain / Alpha-globin


Mass: 15683.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80043
#2: Protein Hemoglobin subunit beta / Hemoglobin beta chain / Beta-globin


Mass: 16153.368 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trematomus bernacchii (emerald rockcod) / References: UniProt: P80044
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6
Details: Crystallization of oxidized Hb from trematomus bernacchii was carried out in capillary at pH6 and room temperature by liquid diffusion technique (final crystallization conditions were 1.5 ...Details: Crystallization of oxidized Hb from trematomus bernacchii was carried out in capillary at pH6 and room temperature by liquid diffusion technique (final crystallization conditions were 1.5 mg/ml protein and 8% w/v MPEG 5K)., pH 6.0, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→13.9 Å / Num. all: 69281 / Num. obs: 69281 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.175 / % possible all: 88.1

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 2H8F

2h8f


Resolution: 1.73→13.9 Å
Isotropic thermal model: Isotropic. Anisotropic thermal model has been used for iron atoms.
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Please note that the collected diffraction data show pseudo-merohedral twinning. The twin fractions, determined by the algorithm implemented in the progream SHELX is almost 0.50.
RfactorNum. reflectionSelection details
Rfree0.197 4308 RANDOM
Rwork0.152 --
all0.156 69281 -
obs0.156 69281 -
Refinement stepCycle: LAST / Resolution: 1.73→13.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4521 0 172 406 5099

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